Question

INPUT：

$target: ENSG00000097007|ABL1
length: 3075
miRNA : hsa-miR-203
length: 22

mfe: -30.5 kcal/mol
p-value: 0.606919

position:  2745
target 5'   C             G     C 3'
             GUGGUCCUGGACA   CAC    
             CACCAGGAUUUGU   GUG    
miRNA  3' GAU             AAA     5'

我必须去除最后两行，然后为它分配两个数组并读取每个字符并获得如下所示的输出，

剥离后的行应采用以下格式：

   CACCAGGAUUUGU   GUG    
GAU             AAA

如果从line1读取行字符，则应以小写字母打印，如果是第二行，则应为大写字母

程序的最终输出应该是 “GAUcaccaggauuuguAAAgug”

我们尝试读取它的代码并没有像输入

中那样剥离完美对齐的线条

这里是我们使用的代码：

 import fileinput
 import sys
 from sys import argv
 script, filename = argv
 file = open(filename)
 og1 = "AGUUCCUUUGUUUUGGUGACUG"
 pattern = "              "
 pattern1 = "miRNA  3'"
 file = open(filename)
 for line in file:
    if line.startswith(pattern):
        n = file.next()
        # print n[9:],#  bound mirna
        for i in range(0, len(og1)):
            print og1[i],
        print "\n" 
        for j in range(0,len(n)):
            print n[j],'

还有问题的进一步输入

target: ENSG00000142208|ENST00000349310|AKT1
length: 992
miRNA : hsa-miR-125b-5p
length: 22

mfe: -23.9 kcal/mol
p-value: 0.610132

position  168
target 5' C     C               A 3'
           CGCAG   GGGGU   AGGGA    
           GUGUU   UCCCA   UCCCU    
miRNA  3' A     CAA     GAG       5'


target: ENSG00000142208|ENST00000349310|AKT1
length: 992
miRNA : hsa-miR-149-3p
length: 21

mfe: -36.6 kcal/mol
p-value: 0.598318

position  798
target 5' C   UGUC     AGG        G 3'
           CGC    GCCCC   CCCUCCCU    
           GUG    CGGGG   GGGAGGGA    
miRNA  3' C   U        GCA          5'


target: ENSG00000142208|ENST00000349310|AKT1
length: 992
miRNA : hsa-miR-185-5p
length: 22

mfe: -27.8 kcal/mol
p-value: 0.606550

position  733
target 5' C       CUCCC   CAGAUGA        C 3'
           CGGGAGC     CCU       UCUCUCCA    
           GUCCUUG     GGA       AGAGAGGU    
miRNA  3' A       AC      A                5'


target: ENSG00000142208|ENST00000349310|AKT1
length: 992
miRNA : hsa-miR-199a-3p
length: 22

mfe: -21.9 kcal/mol
p-value: 0.611970

position  357
target 5' C      CC   CCU      U    C 3'
           AGCCAG   GC   GGGCUG CUGU    
           UUGGUU   CG   UCUGAU GACA    
miRNA  3' A      ACA                  5'


target: ENSG00000142208|ENST00000349310|AKT1
length: 992
miRNA : hsa-miR-451a
length: 21

mfe: -21.2 kcal/mol
p-value: 0.612523

position  416
target 5' C      UCAACC       A     3'
           CUCAGU      UGGUGGC        
           GAGUCA      ACCAUUG        
miRNA  3' U      UU           CCAAA 5'

Answer 1

file = open(filename)                                          
for segment in file.read().split("\n\ntarget"):                          
    interested_lines = segment.split('\n')[-3:-1]  #Fetch last two lines 
    split1 = interested_lines[0].split()                                 
    split2 = interested_lines[1].split()[2:-1]                           
    for i in range(0,len(split1)<len(split2)):                           
        split1.append("")                                                

    req = ""                                                             
    for i in range(0,len(split2)):                                       
        req += split2[i]+split1[i].lower()                               
    for j in range(i+1,len(split1)):                                     
        req += split1[j]                                                 
    print req

<强>输出

AguguuCAAucccaGAGucccu
CgugUcggggGCAgggaggga
AguccuugACggaAagagaggu
AuugguuACAcgUCUGAUGACA
UgagucaUUaccauugCCAAA

Answer 2

我按行划分，抓住最后两行，然后迭代两行拉链并使用不是" "的字符！

def combinebases(base_data):
    lines = base_data.splitlines()[-2:]
    output = list()
    lines[0] = lines[0].lower()
    for ch1, ch2 in zip(*lines):
        output.append(max(ch1, ch2))
    return ''.join(output[10:-4])

可能更安全的结果是返回：

    return re.search("(?<=miRNA  3' )[augc]+", ''.join(output), re.I).group()

但是，如果每个基本长度都相同，那么正则表达式就会过度。

结果：

>>> txt = """$target: ENSG00000097007|ABL1
length: 3075
miRNA : hsa-miR-203
length: 22

mfe: -30.5 kcal/mol
p-value: 0.606919

position:  2745
target 5'   C             G     C 3'
             GUGGUCCUGGACA   CAC    
             CACCAGGAUUUGU   GUG    
miRNA  3' GAU             AAA     5'"""

>>> combinebases(txt)
'GAUcaccaggauuuguAAAgug'

在python中使用适当的缩进来删除一行

2 个答案: